that is just a wild guess so don't talk like its a fact. you don't know and can't possibly tell what happened without even taking a look at the site nor data.
you just assume things, so that doesn't help the guy. its unlikely that only the homepage link would be deindexed (especially for only sending links to tiers, makes no sense), it could also be the site structure and google simply decided the other pages are more relevant and maybe the main page didn't have enough content (or similar as on another site that ranks). then it could also be the sitemap, it could be some SEO plugin, maybe he set the main page to noindex by accident who knows, there can be many reasons.
@agape801 when you say you checked GWT and there was "nothing in there". what do you mean, no new messages or the site wasn't listed ?
try adding some extra content to the homepage, then ping it and also send some links to the homepage itself no tiers and wait a bit it should come back if the rest of the site is still live.
otherwise make sure you don't have any weird settings like the homepage being set to noindex for some reason lol